OR1D2

olfactory receptor family 1 subfamily D member 2, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 17:3088483-3104422

Previous symbols: [ "OLFR1" ]

Links

ENSG00000184166 ∙ NCBI:4991 ∙ OMIM:164342 ∙ HGNC:8183 ∙ Uniprot:P34982 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OR1D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1D2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in OR1D2

This is a list of pathogenic ClinVar variants found in the OR1D2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-3092228-T-C		not specified	Uncertain significance (Feb 27, 2023)
17-3092261-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-3092267-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-3092540-C-T		not specified	Uncertain significance (Dec 07, 2021)
17-3092593-G-T		not specified	Uncertain significance (Dec 22, 2023)
17-3092634-G-T		not specified	Uncertain significance (Jan 23, 2024)
17-3092681-A-G		not specified	Uncertain significance (Apr 30, 2024)
17-3092693-A-G		not specified	Uncertain significance (Jun 16, 2024)
17-3092733-A-C		not specified	Likely benign (Oct 20, 2021)
17-3092781-G-C		not specified	Uncertain significance (May 01, 2022)
17-3092782-A-G		not specified	Uncertain significance (Feb 27, 2023)
17-3092825-G-T		not specified	Uncertain significance (Dec 15, 2023)
17-3092830-T-G		not specified	Uncertain significance (May 15, 2023)
17-3092836-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-3092946-C-G		not specified	Uncertain significance (Jun 02, 2023)
17-3092946-C-T		not specified	Uncertain significance (Feb 23, 2023)
17-3092971-C-A		not specified	Likely benign (Jul 21, 2022)
17-3092980-T-C		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1D2	protein_coding	protein_coding	ENST00000331459	1	939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000925	0.591	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0736	159	162	0.984	0.00000795	2031
Missense in Polyphen		37	46.069	0.80314		669
Synonymous	-0.0314	69	68.7	1.00	0.00000337	662
Loss of Function	0.488	5	6.33	0.790	3.69e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor which may be involved in sperm chemotaxis. Bourgeonal is a strong chemoattractant for sperm in vitro and is shown to be a strong agonist for OR1D2 in vitro. May also function in olfactory reception. {ECO:0000269|PubMed:12663925, ECO:0000269|PubMed:15458659, ECO:0000269|PubMed:16820410}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0871

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0638

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Olfr412

Gene ontology

• Biological process: chemotaxis;G protein-coupled receptor signaling pathway;single fertilization;sensory perception of smell;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity;identical protein binding